Inteins: Nature's Gift to Protein Chemists

Inteins are auto-processing domains found in organisms from all domains of life. These proteins carry out a process known as protein splicing, which is a multi-step biochemical reaction comprised of both the cleavage and formation of peptide bonds. While the endogenous substrates of protein splicing are specific essential proteins found in intein-containing host organisms, inteins are also functional in exogenous contexts and can be used to chemically manipulate virtually any polypeptide backbone. Given this, protein chemists have exploited various facets of intein reactivity to modify proteins in myriad ways for both basic biological research as well as potential therapeutic applications. Here, we review the intein field, first focusing on the biological context and phylogenetic diversity of inteins, followed by a description of intein structure and biochemical function. Finally, we discuss prevalent inteinbased technologies, focusing on their applications in chemical biology, followed by persistent caveats of intein chemistry and approaches to alleviate these shortcomings. The findings summarized herein describe two and a half decades of research, leading from a biochemical curiosity to the development of powerful protein engineering tools.

Naturally split inteins assemble through a "capture and collapse" mechanism

Split inteins are a class of naturally occurring proteins that carry out protein splicing in trans. The chemical mechanism of protein trans-splicing is well-understood and has been exploited to develop several powerful protein engineering technologies. Split intein chemistry is preceded by efficient molecular recognition between two protomers that become intertwined in their bound state. It is currently unclear how this unique topology is achieved upon fragment association. Using biophysical techniques in conjunction with protein engineering methods, including segmental isotopic labeling, we show that one split intein fragment is partly folded, while the other is completely disordered. These polypeptides capture each other through their disordered regions and form an ordered intermediate with native-like structure at their interface. This intermediate then collapses into the canonical intein fold. This mechanism provides insight into the evolutionary constraints on split intein assembly and should enhance the development of split intein-based technologies.

Pharmacovigilance using clinical notes

With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. We present novel methods that annotate the unstructured clinical notes and transform them into a deidentified patient-feature matrix encoded using medical terminologies. We demonstrate the use of the resulting high-throughput data for detecting drug-adverse event associations and adverse events associated with drug-drug interactions. We show that these methods flag adverse events early (in most cases before an official alert), allow filtering of spurious signals by adjusting for potential confounding, and compile prevalence information. We argue that analyzing large volumes of free-text clinical notes enables drug safety surveillance using a yet untapped data source. Such data mining can be used for hypothesis generation and for rapid analysis of suspected adverse event risk.

Extein residues play an intimate role in the rate-limiting step of protein trans-splicing

Split inteins play an important role in modern protein semisynthesis techniques. These naturally occurring protein splicing domains can be used for in vitro and in vivo protein modification, peptide and protein cyclization, segmental isotopic labeling, and the construction of biosensors. The most well-characterized family of split inteins, the cyanobacterial DnaE inteins, show particular promise, as many of these can splice proteins in less than 1 min. Despite this fact, the activity of these inteins is context-dependent: certain peptide sequences surrounding their ligation junction (called local N- and C-exteins) are strongly preferred, while other sequences cause a dramatic reduction in the splicing kinetics and yield. These sequence constraints limit the utility of inteins, and thus, a more detailed understanding of their participation in protein splicing is needed. Here we present a thorough kinetic analysis of the relationship between C-extein composition and split intein activity. The results of these experiments were used to guide structural and molecular dynamics studies, which revealed that the motions of catalytic residues are constrained by the second C-extein residue, likely forcing them into an active conformation that promotes rapid protein splicing. Together, our structural and functional studies also highlight a key region of the intein structure that can be re-engineered to increase intein promiscuity.

Streamlined expressed protein ligation using split inteins

Chemically modified proteins are invaluable tools for studying the molecular details of biological processes, and they also hold great potential as new therapeutic agents. Several methods have been developed for the site-specific modification of proteins, one of the most widely used being expressed protein ligation (EPL) in which a recombinant α-thioester is ligated to an N-terminal Cys-containing peptide. Despite the widespread use of EPL, the generation and isolation of the required recombinant protein α-thioesters remain challenging. We describe here a new method for the preparation and purification of recombinant protein α-thioesters using engineered versions of naturally split DnaE inteins. This family of autoprocessing enzymes is closely related to the inteins currently used for protein α-thioester generation, but they feature faster kinetics and are split into two inactive polypeptides that need to associate to become active. Taking advantage of the strong affinity between the two split intein fragments, we devised a streamlined procedure for the purification and generation of protein α-thioesters from cell lysates and applied this strategy for the semisynthesis of a variety of proteins including an acetylated histone and a site-specifically modified monoclonal antibody.

Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering

We describe the first systematic study of a family of inteins, the split DnaE inteins from cyanobacteria. By measuring in vivo splicing efficiencies and in vitro kinetics, we demonstrate that several inteins can catalyze protein trans-splicing in tens of seconds rather than hours, as is commonly observed for this autoprocessing protein family. Furthermore, we show that when artificially fused, these inteins can be used for rapid generation of protein α-thioesters for expressed protein ligation. This comprehensive survey of split inteins provides indispensable information for the development and improvement of intein-based tools for chemical biology.

Novel data-mining methodologies for adverse drug event discovery and analysis

An important goal of the health system is to identify new adverse drug events (ADEs) in the postapproval period. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. New opportunities have emerged to harness data sources that have not been used within the traditional framework. This article provides an overview of recent methodological innovations and data sources used to support ADE discovery and analysis.

Translational bioinformatics embraces big data

We review the latest trends and major developments in translational bioinformatics in the year 2011-2012. Our emphasis is on highlighting the key events in the field and pointing at promising research areas for the future. The key take-home points are: • Translational informatics is ready to revolutionize human health and healthcare using large-scale measurements on individuals. • Data-centric approaches that compute on massive amounts of data (often called "Big Data") to discover patterns and to make clinically relevant predictions will gain adoption. • Research that bridges the latest multimodal measurement technologies with large amounts of electronic healthcare data is increasing; and is where new breakthroughs will occur.

Split Inteins: Nature's Protein Ligases

Split inteins carry out a naturally occurring process known as protein trans-splicing, where two protein fragments bind to form a catalytically competent enzyme, then catalyze their own excision and the ligation of their flanking sequences. In the past thirteen years since their discovery, chemists and biologists have utilized split inteins in exogenous contexts for a number of biotechnological applications centered around the formation of native peptide bonds. While many protein trans-splicing technologies have emerged and flourished in recent years, several factors still limit their wide-spread practical use. Here, we discuss the development, applications, and limitations of split intein-based technologies and propose that further advancement in this field will require a more fundamental understanding of split intein structure and function.

Five-year functional outcome analysis of ankle fracture fixation

This study examines retrospectively the functional outcome of patients at 5 years following their ankle fracture surgery using the Olerud-Molander Ankle Score (OMAS) and SF-12 questionnaire. Of 69 patients, 43 were females and 26 males. The mean age was 50.7 years. There were 74 and 26% of Weber 'B' and 'C' fractures, respectively. The mean OMAS was 75.2. About 63% of the patients were still complaining of stiffness, around 45% patients were still complaining of ankle swelling, 50% of patients still had some sort of pain, 39% still thought that they had not fully recovered and 38% did not return to their pre-injury sporting activity. Apart from the age, no significant difference was seen in the OMAS due to gender, fracture type or timing of surgery. Our findings show that many patients who have had surgery for ankle fractures will still have some functional limitations even 5 years after the injury.

HyBrow: a prototype system for computer-aided hypothesis evaluation

MOTIVATION

Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered.

RESULTS

We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology and programs to perform hypothesis design and evaluation. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information.

AVAILABILITY

www.hybrow.org

UK acquired hepatitis E--An emerging problem?

Eight cases of hepatitis E acquired in the UK are reported. These cases presented to an inner city hospital in Birmingham, UK, over a 5-month period in 2005. HEV is considered unusual in the UK and generally occurs after travel to endemic regions. Only five cases of hepatitis E acquired in the UK have been reported in the literature. This series represents an increase in the local incidence of hepatitis E, particularly that of UK-acquired infection. HEV should be considered in all patients with acute hepatitis, irrespective of travel history.

Screening time for extra-capsular proximal femoral fracture fixation; the difference between extra-medullary and intra-medullary implant usage

The aim of this study was to compare the fluoroscopic screening time used for treatment of fractures of the trochanteric region of the femur using two different implant systems. Data were collected from 277 proximal femoral fracture fixations. A dynamic hip screw (DHS) was used in 145, and an intra-medullary hip screw (IMHS) was used in 132. There was no difference between the two groups with respect to age, gender or side. Altogether, there were 42% two parts, 35% were three parts and 23% were four parts extra-capsular neck fractures. There was no statistical difference in ionising radiation exposure in closed reduction of these fractures regardless of the fracture configuration or surgical experience of the surgeon. The mean screening time to implant a DHS in two part fractures was 0.48 min, for three part fractures it was 0.45 min and for four part fractures it was 0.46 min. The mean screening time to implant IMHS was 1.02 min for two part fractures, 0.96 min for three part fractures and 1.03 min for four part fractures. These differences were statistically significant (P < or = 0.05).

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology

SUMMARY

Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes, none of them accept Arabidopsis thaliana data. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user.

AVAILABILITY

http://www.personal.psu.edu/nhs109/Clench

A tool-kit for cDNA microarray and promoter analysis

We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. It allows combining of result files into comprehensive data sets, evaluation of the quality of both technical and biological replicates and row and/or column standardization of data matrices. The second set supports mapping ESTs in the genome, identifying the corresponding genes and recovering their promoters, analyzing promoters for transcription factor binding sites, and visual representation of the results. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/

Critical processing factors affecting rheological behavior of a wax based formulation

The use of a wax-based vehicle is one approach to stabilize a drug which is susceptible to hydrolysis and/or oxidation. The drug used in the study, as a microfine powder, is dispersed in the wax mixture and encapsulated in a soft gelatin capsule. To ensure reproducibility of drug content uniformity and encapsulability of the soft gelatin capsule dosage form, optimal viscosity and lot to lot uniformity of the viscosity of the suspension are required. The objective of the study was to identify the critical processing factors which could affect the rheological behavior of the wax based vehicle. Rheological behavior of the vehicle at temperatures ranging from 15 to 90 degrees C was evaluated using a CSL Rheometer equipped with parallel plates and a shear rate sweep mode, unless otherwise specified. Viscosity vs. temperature profiles of the vehicle were determined using the same conditions at different cooling rates ranging from 1.3 to 20 degrees C per min. Three distinct regions of phase transition of the wax mixture can be seen in the Arrhenius plot: (i) a sol region at temperatures above 50 degrees C, (ii) a transition of gel to sol at temperatures ranging from 30 to 45 degrees C, and (iii) a gel region at temperatures below 30 degrees C. The vehicle in a sol region behaved as a Newtonian fluid, indicating minimal interactions between the hydrocarbon chains of the vehicle. The vehicle in a gel region behaved thixotropic in nature, as indicated by a hysteresis loop. The shear rate had a more pronounced effect on the area of thixotropy than the shear time. The cooling rate had a pronounced effect on the resultant viscosity. At the same applied shear rate, the vehicle which was cooled at a faster rate, may cause a recrystallization of the wax mixture in different crystalline forms, resulting in a higher viscosity than the vehicle cooled at a slower rate. This effect was more pronounced when the shear was applied at a lower rate. The results of this study indicate that shear rate and cooling rate are the critical processing factors in controlling the viscosity of the final product and must be well controlled in the manufacturing procedure.

Safety and efficacy of an oil-adjuvant vaccine against haemorrhagic septicaemia in buffalo calves: cross-protection between the serotypes B:2,5 and E:2,5

The safety, efficacy and duration of immunity of an improved oil-adjuvant vaccine against haemorrhagic septicaemia, containing inactivated cells of Pasteurella multocida serotype B:2,5, were tested in young buffalo calves in Pakistan. For safety testing, five buffalo calves were vaccinated intramuscularly with twice the normal dose, and six weeks later with a normal dose. Except for a transient rise in rectal temperature at six hours after the vaccinations, no systemic reactions were observed. The buffaloes remained in good condition and had a normal appetite. No local reactions were observed at the injection site. For efficacy testing two trials were carried out. In the first, buffalo calves were vaccinated intramuscularly either with two doses two-and-a-half months apart, or with a single dose, or left unvaccinated. They were challenged subcutaneously with virulent P multocida after eight, 13 or 15 months. After challenge at eight months the four buffaloes given two doses and the buffalo given one dose were protected, whereas the control animal developed the typical signs of the disease. After the challenges at 13 and 15 months, the vaccinated animals were still protected whereas the control animals died. In the second trial, buffalo calves were vaccinated intramuscularly either with two doses two months apart, or with a single dose at two months or left unvaccinated. The buffaloes were challenged after eight or 14 months. After challenge at eight months the four control animals died, whereas three of the four buffaloes given a single dose were protected. After challenge at 14 months, the three control animals died, whereas four of the five buffaloes given two doses and both the buffaloes given a single dose were protected. To test for cross-protection against the heterologous serotypes E:2,5 and B:3,4, groups of mice were vaccinated once or left unvaccinated. Four weeks later, the vaccinated and control groups were challenged with a dilution series of the different challenge cultures. The vaccine appeared to induce protection against challenge with different strains of serotypes B:2,5 and E:2,5 but not against strains of serotype B:3,4.